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Hi, Like the title says, xdrawchem-1.9.9 fails to build against openbabel-2.2.0_beta4. I just recompile finish rebuilding my entire system (emerge -eN system && emerge -eN world). I provided the error messages in the Actual result section. Any ideas? Thanks Paul Reproducible: Always Steps to Reproduce: 1.emerge =sci-chemistry/openbabel-2.2.0_beta 2.emerge =sci-chemistry/xdrawchem-1.9.9 3. Actual Results: if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -I/usr/X11R6/include -DUNIX -DRINGHOME="\"/usr/share/xdrawchem/\"" -DXDC_SERVER=\"www.xdrawchem.org\" -I/usr/include/openbabel-2.0 -g -I/usr/qt/3/include -g -march=pentium4 -O3 -pipe -fomit-frame-pointer -MT application_ob.o -MD -MP -MF ".deps/application_ob.Tpo" -c -o application_ob.o application_ob.cpp; \ then mv -f ".deps/application_ob.Tpo" ".deps/application_ob.Po"; else rm -f ".deps/application_ob.Tpo"; exit 1; fi application_ob.cpp: In member function 'void ApplicationWindow::OBGetFilters()': application_ob.cpp:48: error: 'Formatpos' was not declared in this scope application_ob.cpp:48: error: expected `;' before 'pos' application_ob.cpp:51: error: 'GetNextFormat' is not a member of 'OpenBabel::OBConversion' make[2]: *** [application_ob.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/work/xdrawchem-1.9.9/xdrawchem' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/work/xdrawchem-1.9.9' make: *** [all] Error 2 * * ERROR: sci-chemistry/xdrawchem-1.9.9 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 1029: Called die * The specific snippet of code: * emake || die "emake failed." * The die message: * emake failed. * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/temp/environment'. * * Messages for package sci-chemistry/xdrawchem-1.9.9: * * ERROR: sci-chemistry/xdrawchem-1.9.9 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 1029: Called die * The specific snippet of code: * emake || die "emake failed." * The die message: * emake failed. * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/xdrawchem-1.9.9/temp/environment'. * * GNU info directory index is up-to-date. Expected Results: completed compilation and installation emerge --info Portage 2.1.4.4 (default-linux/x86/2007.0/desktop, gcc-4.2.3, glibc-2.7-r2, 2.6.24-gentoo-r2 i686) ================================================================= System uname: 2.6.24-gentoo-r2 i686 Intel(R) Pentium(R) 4 CPU 2.80GHz Timestamp of tree: Fri, 28 Mar 2008 22:30:02 +0000 app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.5 dev-lang/python: 2.5.1-r5 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.24 ACCEPT_KEYWORDS="x86 ~x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=pentium4 -O3 -pipe -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=pentium4 -O3 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="ccache cvs distcc distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch userpriv usersandbox" GENTOO_MIRRORS="ftp://ftp.nrc.ca/pub/systems/linux/gentoo/ http://mirror.tucdemonic.org/gentoo/ ftp://gentoo.netnitco.net/pub/mirrors/gentoo/source/ http://gentoo.netnitco.net ftp://ftp.ussg.iu.edu/pub/linux/gentoo" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/portage/local/layman/science /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X aac aalib acl acpi alsa ansi arts berkdb cairo cdr cli cracklib crypt cups dbus divx4linux dri dvd dvdr dvdread eds emboss encode esd evo faad2 fam fbdev firefox flac fortran gcj gdbm gif gnome gpm gstreamer gtk hal iconv ipv6 isdnlog java jpeg kde kerberos ldap live m4a mad midi mikmod mp3 mp4 mpeg mudflap nas ncurses network nls nptl nptlonly ogg opengl openmp oss pam pcre pdf perl png pppd python qt3 qt3support qt4 quicktime readline reflection sdl seamonkey session spell spl ssl svg tcpd tiff truetype unicode vorbis win32codecs wma wmv x86 xml xorg xv zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="vesa vga fbdev nv nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created an attachment (id=148423) [edit] The build log Here is the complete build log
Thanks much for your bug report. Unfortunately, it looks like there's quite a bit of breakage with openbabel-2.2.0. I'll have a look but this may be quite difficult to fix. best, Markus
I've changed the dependencies to <openbabel-2.2 for now until we've sorted this out. openbabel-2.0 and 2.1 seem to work fine for me. Markus
fwiw I've been working on openbabel as much as I can, it's a can of worms.
cryos is one of the openbabel devs (I think) and I'll email him later to ask how to best replace the GetNextFormat API function that is missing in openbabel-2.2 and causes the xdrawchem compile to bomb. It should be fairly trivial for somebody who knows the openbabel API I would assume. If he doesn't know, I can probably fix it myself, since xdrawchem's upstream seems pretty dead. cheers, Markus
Only just come across this - I will take a look and see what I can do.
Could you elaborate on the breakage in 2.2 too? We are working on getting the 2.2 release out and obviously I would like to correct any breakage before the release if possible. The API should not be broken and where it is I will see about correcting that (or talking to the people who can).
Take a look at openbabel-2.2.0_beta4-r1 and the patch it applies - fixes it here. If it looks good I will see about getting this applied upstream before the release of OpenBabel 2.2. Please do let me know about any other issues with OpenBabel 2.2 too.
Hi Marcus, I just peeked at your api patch in openbabel-2.2.0_beta4-r1 and it looks like it contains exactly what what missing before, i.e. the member definition for GetNextFormat. I haven't tried compiling xdrawchem yet, but I think this should fix it. Thanks much, Markus
Between Chris Morley and myself upstream is now patched in a slightly different way. Hopefully there will be another beta release very soon, if not I might do a snapshot.... Now is the time to let me/the OpenBabel community know about any issues before the 2.2 release. If you know of any other problems I would really appreciate you letting me know sooner rather than later. Hopefully everything else looks good and there are no more API breaks.
Hi Marcus, xdrawchem builds fine for me against openbabel-2.2.0_beta-r1. Thanks! The only additional issue with openbabel I am aware of is #212526 but I haven't looked into it enough to be able to judge if it is a problem with openbabel's build system in general or gentoo specific. Best, Markus
I'm thinking of bugs #212212 and #206574.
Should I file this as a separate bug, or is it being here enough? config.status: executing depfiles commands config.status: executing include/openbabel/babelconfig.h commands Makefile:156: *** missing separator. Stop. * * ERROR: sci-chemistry/openbabel-2.2.0_beta4-r1 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 2176: Called die * The specific snippet of code: * emake || die "emake failed"; * The die message: * emake failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-chemistry/openbabel-2.2.0_beta4-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/openbabel-2.2.0_beta4-r1/temp/environment'. * Shingoshi
Created an attachment (id=151797) [edit] Build.log and emerge --info
This is the wx-widgets wx-config problem. It is in a separate bug (forget which one right now and am on the way out the door). You can run wx-config to fix this one, this should get fixed in the next release.
This should be fixed in openbabel-2.2.0. Thanks, Markus
